devtools::install()
## Skipping 2 packages not available: pasilla, DESeq2
##
checking for file ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/RPackages/ContrApption/DESCRIPTION’ ...
✓ checking for file ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/RPackages/ContrApption/DESCRIPTION’
##
─ preparing ‘ContrApption’: (735ms)
##
checking DESCRIPTION meta-information ...
✓ checking DESCRIPTION meta-information
##
─ checking for LF line-endings in source and make files and shell scripts (336ms)
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─ checking for empty or unneeded directories
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─ building ‘ContrApption_0.0.1.9000.tar.gz’
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##
Running /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL \
## /var/folders/g0/2sgkg3j573v5c8tt_dqgkjmw0000gp/T//RtmpN3g7uh/ContrApption_0.0.1.9000.tar.gz \
## --install-tests
## * installing to library ‘/Users/Thadryan/Dropbox (Partners HealthCare)/Workspace/HFrEF_v_HFpEF_FullModel/renv/library/R-3.6/x86_64-apple-darwin15.6.0’
## * installing *source* package ‘ContrApption’ ...
## ** using staged installation
## ** R
## ** inst
## ** byte-compile and prepare package for lazy loading
## ** help
## *** installing help indices
## ** building package indices
## ** installing vignettes
## ** testing if installed package can be loaded from temporary location
## ** testing if installed package can be loaded from final location
## ** testing if installed package keeps a record of temporary installation path
## * DONE (ContrApption)
library(ContrApption)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
suppressMessages(library(DESeq2))
## Warning: package 'S4Vectors' was built under R version 3.6.3
## Warning: package 'GenomeInfoDb' was built under R version 3.6.3
## Warning: package 'DelayedArray' was built under R version 3.6.3
#> Warning: package 'S4Vectors' was built under R version 3.6.3
#> Warning: package 'GenomeInfoDb' was built under R version 3.6.3
#> Warning: package 'DelayedArray' was built under R version 3.6.3
suppressMessages(library(pasilla))
# loads sample annotation from the pasilla package
pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv", package = "pasilla", mustWork = TRUE)
# read in the sample data
coldata <- read.csv(pasAnno, row.names = 1)
# select relevant columns
coldata <- data.frame(coldata[ , c("condition","type")])
# remove un-needed characters
rownames(coldata) <- gsub("fb", "", rownames(coldata))
# loads counts file from the pasilla package
pasCts <- system.file("extdata", "pasilla_gene_counts.tsv", package = "pasilla", mustWork = TRUE)
# reads counts of genes
cts <- read.csv(pasCts, sep = "\t", row.names = "gene_id")
# make sure the order is correct
cts <- cts[, rownames(coldata)]
# create a DESeq2 dataset from the metadata and counts
dds <- DESeq(DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition))
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
normCounts <- counts(dds, normalized = TRUE)
res <- results(dds, tidy = TRUE) %>%
data.frame %>%
filter(padj < 0.05)
normCountsSig <- normCounts %>%
data.frame %>%
filter(rownames(.) %in% res$row)
ContrApption(data = normCountsSig, annotation = coldata)
Please don’t write over me!
# devtools::install(); library(ContrApption); ContrApption(data = normCountsSig, annotation = coldata)
ContrApption(data = normCountsSig, annotation = coldata)